Uncultured Specimens Research Articles

Broad-Spectrum Biosensor Capable of Detecting and Identifying Diverse Bacterial and Candida Species in Blood

We describe an assay which uses broad-spectrum, conserved-site PCR paired with mass spectrometry analysis of amplicons (PCR/electrospray ionization-mass spectrometry [ESI-MS]) to detect and identify diverse bacterial and Candida species in uncultured specimens. The performance of the assay was characterized using whole-blood samples spiked with low titers of 64 bacterial species and 6 Candida species representing the breadth of coverage of the assay. The assay had an average limit of detection of 100 CFU of bacteria or Candida per milliliter of blood, and all species tested yielded limits of detection between 20 and 500 CFU per milliliter. Over 99% of all detections yielded correct identifications, whether they were obtained at concentrations well above the limit of detection or at the lowest detectable concentrations. This study demonstrates the ability of broad-spectrum PCR/ESI-MS assays to detect and identify diverse organisms in complex natural matrices that contain high levels of background DNA.

Neurotrophin 4 enhances in vitro follicular assembly in human fetal ovaries

To investigate the in vitro effect of neurotrophin 4 (NT-4) on follicular assembly in human fetal ovaries. Human ovarian tissue from fetuses at 19-20 gestational weeks was placed in organ culture for two weeks with NT-4. Control groups were cultured with a neutralizing antibody against NT-4. Infertility unit at an university-affiliated tertiary medical center. Four patients who underwent pregnancy terminations at 19-20 gestational weeks. None. Histologic findings of follicular assembly. Follicular assembly was significantly increased in the specimens cultured with NT-4 than in the uncultured specimens, the samples cultured without NT-4, and samples cultured with the neutralizing antibody. In the second week of culture, additional follicular assembly was promoted in the presence of 100 ng/mL NT-4 but not with 10 ng/mL NT-4. This is the first report showing that NT-4 seems to promote human follicular assembly in fetal ovaries, probably in a dose-dependent manner. Follicular assembly is regulated by multiple signals, and additional studies on the effects of other growth factors in combination with NT-4 are warranted.

Detection of low-level mosaicism and placental mosaicism by oligonucleotide array comparative genomic hybridization

PurposeTo determine the sensitivity of whole-genome oligonucleotide array comparative genomic hybridization for the detection of mosaic cytogenetic abnormalities. MethodsMosaicism sensitivity was evaluated by testing artificially derived whole chromosome and segmental aneuploidies ranging from 0% to 100% abnormal and additional naturally occurring mosaic specimens. ResultsUsing combined dye-reversed replicates and an unfiltered analysis, oligonucleotide array comparative genomic hybridization detected as low as 10% and 20–30% mosaicism from whole chromosome and segmental aneuploidies, respectively. To investigate discrepancies between cultured and uncultured specimens, array comparative genomic hybridization was performed on DNA from additional direct product of conception specimens with abnormal karyotypes in culture. Interestingly, 5 of 10 product of conception specimens with double trisomies on cultured cell analysis had only a single trisomy by array comparative genomic hybridization and quantitative polymerase chain reaction on DNA from the uncultured direct specimen, and all harbored the more commonly observed trisomy. Thus, oligonucleotide array comparative genomic hybridization revealed previously unidentified placental mosaicism in half of the products of conception with double-aneuploid conventional karyotypes. ConclusionOligonucleotide array comparative genomic hybridization can detect low-level mosaicism for whole chromosome (∼10%) and segmental (∼20–30%) aneuploidies when using specific detection criteria. In addition, careful interpretation is required when performing array comparative genomic hybridization on DNA isolated from direct specimens as the results may differ from the cultured chromosome analysis.

Effects of basic fibroblast growth factor on in vitro development of human ovarian primordial follicles

To evaluate whether basic fibroblast growth factor (FGF) benefits the in vitro development of human primordial follicles. Human ovarian tissue was placed in organ culture for 4 weeks with basic FGF and either fetal calf serum or a serum-free combination. Control groups were cultured with a neutralizing antibody against basic FGF. Major tertiary care and referral academic centers. Fourteen women/girls undergoing various gynecological operations and two fetuses from women undergoing pregnancy terminations. None. Follicular counts, immunohistochemistry for proliferating cell nuclear antigen and bromodeoxyuridine incorporation and measurement of 17beta E(2) production. Only in the serum-free culture system was the number of developing follicles in samples cultured with basic FGF significantly higher than in uncultured specimens. The E(2) production increased significantly in the second week, and there was a significant reduction in E(2) secretion with the addition of the neutralizing antibody against basic FGF. The percentage of granulosa cells (GCs) that stained for proliferating cell nuclear antigen or bromodeoxyuridine was significantly higher in developing follicles than in primordial follicles, regardless of treatment. Basic FGF apparently plays a role in the E(2) production of early follicles. High doses of basic FGF enhanced follicular development in serum-free media.

Relative efficiency of FISH on metaphase and interphase nuclei from non-mosaic trisomic or triploid fibroblast cultures.

Chromosome specific probes that are used in interphase fluorescence in situ hybridization (FISH) analysis are usually tested on disomic control samples. When used for preimplantation or prenatal diagnosis the aim is to detect aneuploidy, most frequently trisomy. In this study, skin fibroblast cultures from non-mosaic trisomic and triploid fetuses were analysed by FISH to assess probe efficiency regarding interphase detection of trisomy. Skin fibroblast cultures were used because they are considered to be stable in culture. FISH experiments were performed using centromeric probes for chromosomes X, Y, 18 and locus specific probes for chromosomes 13 and 21. In metaphase nuclei, the expected signals were found in 100% of at least 30 metaphases counted on each sample and this also confirmed non-mosaicism in agreement with conventional karyotyping of the fetuses. On interphase nuclei, however, only 80-89% of nuclei per population displayed the expected signals for autosomal probes and 90% for probes for the sex chromosomes. For each probe, a range of percentages was obtained that can be regarded as indicative of non-mosaic trisomy in uncultured specimens. In the case of prenatal samples, the expected presence of maternal cells may lead to a lowering of the threshold for a trisomic diagnosis. In the case of preimplantation diagnosis, the accuracy can be improved by the use of two probes per chromosome or by the analysis of two cells from each embryo.

Mutation and Allelic Loss of the PTEN/MMAC1 gene in Primary and Metastatic Melanoma Biopsies

The PTEN/MMAC1 gene on chromosome 10q23 encodes a lipid phosphatase with tumor-suppressive properties. Germline PTEN/MMAC1 mutations have been implicated as the predisposing factor in Cowden disease and other hamartoma syndromes, and somatic mutations and deletions have been identified in a wide range of human cancers, including 30-40% of metastatic melanoma cell lines. To study further the possible role of PTEN/MMAC1 in the pathogenesis and progression of malignant melanoma, we examined uncultured specimens from 16 primary and 61 metastatic tumors from 67 patients. Denaturing gradient gel electrophoresis was used to analyze systematically the coding region of PTEN/MMAC1 and revealed mutations in four of the metastatic samples (7%). Sequence analysis of the mutants identified a 1 bp frameshift insertion, a 2 bp frameshift deletion, an 11 bp frameshift deletion, and a single base substitution resulting in the generation of a premature stop codon. Analysis of two intragenic polymorphisms showed allelic loss in three of eight informative primary tumors (38%) and in 18 of 31 metastatic tumors (58%). One of the mutant cases showed allelic loss, suggesting that both PTEN/MMAC1 alleles were inactivated in this tumor. Altogether, these results suggest that mutation and deletion of PTEN/MMAC1 may contribute to the development and progression of malignant melanoma.

Detection and rapid differentiation of human enteroviruses following genomic amplification.

By employing a nested PCR (n-PCR) with specific primers derived from the 5' nontranslated and consensus region of the human enterovirus genome, we detected enterovirus RNA from 32 different serotypes of prototypic strains. A specific 297-bp fragment was amplified by this method from all of these strains. Not only was the method highly sensitive, detecting enterovirus RNA extracted from 0.01 50% tissue culture infective dose/50 microl (which is more sensitive than our current routine method of enterovirus diagnosis, based on the virus isolation and serotypic neutralization), but it was also relatively rapid. By using this technology, we also detected enterovirus RNA in uncultured specimens (including throat swabs and stools) from patients with respiratory illness and acute flaccid paralysis syndrome. This method enabled us to rapidly and directly distinguish enterovirus-infected specimens from nonenterovirus specimens in laboratory diagnosis. Furthermore, restriction fragment length polymorphism was assessed as an alternative means of differentiating various serotypes of prototypical enteroviruses. Fourteen of 16 human enterovirus-infected specimens exhibited restriction patterns identical to those of the corresponding prototypes.

Prenatal diagnosis of trisomy 9: cytogenetic, FISH, and DNA studies

A cytogenetic survey and follow-up studies were performed in eight cases of full, mosaic, and pseudomosaic trisomy 9 prenatally diagnosed among 36,213 prenatal samples in our department between August 1970 and July 1996. Besides conventional chromosome analysis, interphase fluorescent in situ hybridization (FISH) was employed. FISH turned out to be a rapid and accurate method for verification of trisomy cell lines and could provide additional information to the prenatal cytogenetic results. FISH also enables the study of uncultured specimens of amniotic fluid, not accessible for traditional cytogenetic analysis. In three cases, retrospective DNA analysis showed the supernumerary chromosome 9 to be of maternal origin. The disomic cell lines in both mosaic trisomy 9 cases showed maternal uniparental disomy.

Cytogenetic abnormalities are frequent in uncultured prostate cancer cells

Despite attempts by several laboratories to identify consistent chromosome abnormalities in cancer of the prostate, relatively few clonal changes have been found. We compared analysis of metaphases from uncultured specimens of primary prostate cancer (direct preparations) with those obtained from short-term culture using various media. While the number of metaphases in uncultured specimens was low, and chromosome morphology fair to poor, structural chromosome changes could be identified as clonal in 5 of 14 specimens (36%). In contrast, while clonal abnormalities were found in 20 of 61 (33%) specimens analyzed after short-term culture, these abnormalities were predominantly numerical and simple structural changes. Two tumors metastatic to lymph nodes were studied using direct preparations; both were near tetraploid, with multiple structural abnormalities, including isochromosome 8q in both and del(8)(p21) in one. Cytogenetic analyses of metastatic prostate tumors have been very limited, and these data suggest that formation of an i(8q) may be the mechanism by which loss of heterozygosity of 8p, reported frequently in molecular analyses, occurs. Our findings indicate that prostate cancers, like most solid tumors, do have clonal chromosome abnormalities that are frequently complex, but the method that reproducibly yields representative karyotypes from this particular tumor remains to be identified.

Characterization of a Mycobacterium tuberculosis insertion sequence, IS6110, and its application in diagnosis

An insertion sequence-like element, IS6110, was isolated from a Mycobacterium tuberculosis cosmid library as a repetitive sequence. IS6110 shows similarities with elements of the IS3 family. This insertion sequence was found to be specific to mycobacteria belonging to the M. tuberculosis complex. For detection and identification of M. tuberculosis bacilli in uncultured specimens, oligonucleotides derived from the IS6110 sequence were used as primers and probes in polymerase chain reaction studies. The results obtained were consistent with results of classical identification procedures, bacteriological data, and clinical criteria.

Control of brush border enzymes by dexamethasone in the fetal rat intestine cultured in vitro.

The effect of dexamethasone (DX) on the prenatal maturation of rat intestinal brush border enzymes was studied in organ culture. Jejunal segments were explanted daily from day 17 of gestation until birth, as well as at different postnatal stages until day 6; they were cultured for 48 h with or without DX (8 X 10(-8) M). Enzymatic activities were analyzed on brush border membranes purified from cultured intestines and were compared with values from uncultured specimens. The results showed that DX elicited (a) a precocious induction of sucrase activity in the jejunum explanted from 19 days of gestation onward, reaching a peak value when taken at birth; (b) a stimulation of maltase activity in the segments explanted as soon as day 18, leading to maximal values when taken at day 20, the stage at which the stimulated activity reached a 6.5-fold increase over the baseline activity; and (c) an increase of lactase activity comparable to that occurring in utero. As opposed to this, DX has no specific action on alkaline phosphatase and aminopeptidase activities. The present data indicate that glucocorticoids directly and specifically influence the prenatal maturation of some brush border enzymes in the mammalian gut.

Search for type‐c oncornavirus–related genetic information in tissues from patients with systemic lupus erythematosus

Single-stranded 3H-DNA probes complementary to the RNA of Rauscher murine leukemia virus and of simian sarcoma virus were prepared using techniques that permitted complete transcription of the viral genome of each virus. These probes were used in DNA-DNA hybridization studies with the cellular DNA from uncultured specimens of spleens and placentas of patients with systemic lupus erythematosus (SLE). No proviral DNA sequences related to these viruses were detected in these tissues. The results presented here do not support previously reported antigenic data implicating type-C oncornavirus infection of these organs in SLE.